Tools¶
Convex hull construction¶
This module provides the ConvexHull class.

class
icet.tools.convex_hull.
ConvexHull
(concentrations, energies)[source]¶ This class provides functionality for extracting the convex hull of the (free) energy of mixing. It is based on the convex hull calculator in SciPy.
Parameters:  concentrations (list(float) or list(list(float))) – concentrations for each structure listed as
[[c1, c2], [c1, c2], ...]
; for binaries, in which case there is only one independent concentration, the format[c1, c2, c3, ...]
works as well.  energies (list(float)) – energy (or energy of mixing) for each structure

concentrations
¶ concentrations of the N structures on the convex hull
Type: np.ndarray

energies
¶ energies of the N structures on the convex hull
Type: np.ndarray

dimensions
¶ number of independent concentrations needed to specify a point in concentration space (1 for binaries, 2 for ternaries etc.)
Type: int

structures
¶ indices of structures that constitute the convex hull (indices are defined by the order of their concentrations and energies are fed when initializing the ConvexHull object)
Type: list(int)
Examples
A ConvexHull object is easily initialized by providing lists of concentrations and energies:
hull = ConvexHull(data['concentration'], data['mixing_energy'])
after which one can for example plot the data (assuming a matplotlib axis object
ax
):ax.plot(hull.concentrations, hull.energies)
or extract structures at or close to the convex hull:
low_energy_structures = hull.extract_low_energy_structures( data['concentration'], data['mixing_energy'], tolerance=0.005, structures=list_of_structures)
A complete example can be found in the basic tutorial.

extract_low_energy_structures
(concentrations, energies, energy_tolerance, structures=None)[source]¶ Returns structures that lie within a certain tolerance of the convex hull.
Parameters:  concentrations (
Union
[List
[float
],List
[List
[float
]]]) –concentrations of candidate structures
If there is one independent concentration, a list of floats is sufficient. Otherwise, the concentrations must be provided as a list of lists, such as
[[0.1, 0.2], [0.3, 0.1], ...]
.  energies (
List
[float
]) – energies of candidate structures  energy_tolerance (
float
) – include structures with an energy that is at most this far from the convex hull  structures (
Optional
[list
]) –list of candidate structures, e.g.,
ASE Atoms
objects, corresponding toconcentrations
andenergies
The list will be returned, but with the objects too far from the convex hull removed. If None, a list of indices is returned instead.
Return type: List
[int
] concentrations (

get_energy_at_convex_hull
(target_concentrations)[source]¶ Returns the energy of the convex hull at specified concentrations. If any concentration is outside the allowed range, NaN is returned.
Parameters: target_concentrations ( Union
[List
[float
],List
[List
[float
]]]) –concentrations at target points
If there is one independent concentration, a list of floats is sufficient. Otherwise, the concentrations ought to be provided as a list of lists, such as
[[0.1, 0.2], [0.3, 0.1], ...]
.Return type: ndarray
 concentrations (list(float) or list(list(float))) – concentrations for each structure listed as
Mapping structures¶

icet.tools.structure_mapping.
map_structure_to_reference
(input_structure, reference_structure, tolerance_mapping, vacancy_type=None, inert_species=None, tolerance_cell=0.05, tolerance_positions=0.01)[source]¶ Maps a relaxed structure onto a reference structure. The function returns a tuple comprising
 the ideal supercell most closely matching the input structure,
 the largest deviation of any input coordinate from its ideal coordinate, and
 the average deviation of the input coordinates from the ideal coordinates.
Parameters:  input_structure (
Atoms
) – relaxed input structure  reference_structure (
Atoms
) – reference structure, which can but need not represent the primitive cell  tolerance_mapping (
float
) –maximum allowed displacement for mapping an atom in the relaxed (but rescaled) structure to the reference supercell
Note: A reasonable choice is up to 2030% of the first nearest neighbor distance (r1). A value above 50% of r1 will most likely lead to atoms being multiply assigned, whereby the mapping fails.
 vacancy_type (
Optional
[str
]) –If this parameter is set to a nonzero string unassigned sites in the reference structure will be assigned to this type.
Note 1: By default (
None
) the method will fail if there are any unassigned sites in the reference structure.Note 2:
vacancy_type
must be a valid species as enforced by thease.Atoms
class.  inert_species (
Optional
[List
[str
]]) – List of chemical symbols (e.g.,['Au', 'Pd']
) that are never substituted for a vacancy. Used to make an initial rescale of the cell and thus increases the probability for a successful mapping. Need not be specified ifvacancy_type
isNone
.  tolerance_cell (
float
) – tolerance factor applied when computing permutation matrix to generate supercell  tolerance_positions (
float
) – tolerance factor applied when scanning for overlapping positions in Angstrom (forwarded toase.build.cut()
)
Example
The following code snippet illustrates the general usage. It first creates a primitive FCC cell, which is latter used as reference structure. To emulate a relaxed structure obtained from, e.g., a density functional theory calculation, the code then creates a 4x4x4 conventional FCC supercell, which is populated with two different atom types, has distorted cell vectors, and random displacements to the atoms. Finally, the present function is used to map the structure back the ideal lattice:
from ase.build import bulk reference = bulk('Au', a=4.09) atoms = bulk('Au', cubic=True, a=4.09).repeat(4) atoms.set_chemical_symbols(10 * ['Ag'] + (len(atoms)  10) * ['Au']) atoms.set_cell(atoms.cell * 1.02, scale_atoms=True) atoms.rattle(0.1) mapped_atoms = map_structure_to_reference(atoms, reference, 1.0)
Return type: Tuple
[Atoms
,float
,float
]
Structure enumeration¶

icet.tools.structure_enumeration.
enumerate_structures
(atoms, sizes, chemical_symbols, concentration_restrictions=None, niggli_reduce=None)[source]¶ Yields a sequence of enumerated structures. The function generates all inequivalent structures that are permissible given a certain lattice. Using the
chemical_symbols
andconcentration_restrictions
keyword arguments it is possible to specify which chemical_symbols are to be included on which site and in which concentration range.The function is sensitive to the boundary conditions of the input structure. An enumeration of, for example, a surface can thus be performed by setting
atoms.pbc = [True, True, False]
.The algorithm implemented here was developed by Gus L. W. Hart and Rodney W. Forcade in Phys. Rev. B 77, 224115 (2008) [HarFor08] and Phys. Rev. B 80, 014120 (2009) [HarFor09].
Parameters:  atoms (
Atoms
) – primitive structure from which derivative superstructures should be generated  sizes (
List
[int
]) – number of sites (included in enumeration)  chemical_symbols (
list
) – chemical species with which to decorate the structure, e.g.,['Au', 'Ag']
; see below for more examples  concentration_restrictions (
Optional
[dict
]) – allowed concentration range for one or more element in chemical_symbols, e.g.,{'Au': (0, 0.2)}
will only enumerate structures in which the Au content is between 0 and 20 %; here, concentration is always defined as the number of atoms of the specified kind divided by the number of all atoms.  niggli_reduction – if True perform a Niggli reduction with spglib for each
structure; the default is
True
ifatoms
is periodic in all directions,False
otherwise.
Examples
The following code snippet illustrates how to enumerate structures with up to 6 atoms in the unit cell for a binary alloy without any constraints:
from ase.build import bulk prim = bulk('Ag') enumerate_structures(atoms=prim, sizes=range(1, 7), chemical_symbols=['Ag', 'Au'])
To limit the concentration range to 10 to 40% Au the code should be modified as follows:
enumerate_structures(atoms=prim, sizes=range(1, 7), chemical_symbols=['Ag', 'Au'], concentration_restrictions={'Au': (0.1, 0.4)})
Often one would like to consider mixing on only one sublattice. This can be achieved as illustrated for a Ga(1x)Al(x)As alloy as follows:
prim = bulk('GaAs', crystalstructure='zincblende', a=5.65) enumerate_structures(atoms=prim, sizes=range(1, 9), chemical_symbols=[['Ga', 'Al'], ['As']])
Return type: Atoms
 atoms (

icet.tools.structure_enumeration.
enumerate_supercells
(atoms, sizes, niggli_reduce=None)[source]¶ Yields a sequence of enumerated supercells. The function generates all inequivalent supercells that are permissible given a certain lattice. Any supercell can be reduced to one of the supercells generated.
The function is sensitive to the boundary conditions of the input structure. An enumeration of, for example, a surface can thus be performed by setting
atoms.pbc = [True, True, False]
.The algorithm is based on Gus L. W. Hart and Rodney W. Forcade in Phys. Rev. B 77, 224115 (2008) [HarFor08] and Phys. Rev. B 80, 014120 (2009) [HarFor09].
Parameters:  atoms (
Atoms
) – primitive structure from which supercells should be generated  sizes (
List
[int
]) – number of sites (included in enumeration)  niggli_reduction – if True perform a Niggli reduction with spglib for each
supercell; the default is
True
ifatoms
is periodic in all directions,False
otherwise.
Examples
The following code snippet illustrates how to enumerate supercells with up to 6 atoms in the unit cell:
from ase.build import bulk prim = bulk('Ag') enumerate_supercells(atoms=prim, sizes=range(1, 7))
Return type: Atoms
 atoms (

icet.tools.structure_enumeration.
get_symmetry_operations
(atoms, tolerance=0.001)[source]¶ Returns symmetry operations permissable for a given structure as obtained via spglib. The symmetry operations consist of three parts: rotation, translation and basis shifts. The latter define the way that sublattices shift upon rotation (correponds to d_Nd in [HarFor09]).
Parameters:  atoms (
Atoms
) – structure for which symmetry operations are sought  tolerance (
float
) – numerical tolerance imposed during symmetry analysis
Return type: Dict
[str
,list
] atoms (
Structure generation and SQS¶

icet.tools.structure_generation.
generate_sqs
(cluster_space, max_size, target_concentrations, include_smaller_cells=True, T_start=5.0, T_stop=0.001, n_steps=None, optimality_weight=1.0, random_seed=None, tol=1e05)[source]¶ Given a
cluster_space
, generate a special quasirandom structure (SQS), i.e., a structure that for a given supercell size provides the best possible approximation to a random alloy [ZunWeiFer90].In the present case, this means that the generated structure will have a cluster vector that as closely as possible matches the cluster vector of an infintely large randomly decorated supercell. Internally the function uses a simulated annealing algorithm and the difference between two cluster vectors is calculated with the measure suggested by A. van de Walle et al. in Calphad 42, 1318 (2013) [WalTiwJon13] (for more information, see
mchammer.calculators.TargetVectorCalculator
).Parameters:  cluster_space (
ClusterSpace
) – a cluster space defining the lattice to be decorated.  max_size (
int
) – maximum supercell size  target_concentrations (
dict
) –concentration of each species in the target structure (for example
{'Ag': 0.5, 'Pd': 0.5}
Concentrations are always expressed with respect to all atoms in the supercell, which implies that the sum of all concentrations should always be 1. In the case of multiple sublattices, a valid specification would thus be
{'Au': 0.25, 'Pd': 0.25, 'H': 0.1, 'V': 0.4}
.  include_smaller_cells (
bool
) – if True, search among all supercell sizes includingmax_size
, else search only among those exactly matchingmax_size
 T_start (
float
) – artificial temperature at which the simulated annealing starts  T_stop (
float
) – artifical temperature at which the simulated annealing stops  n_steps (
Optional
[float
]) – total number of Monte Carlo steps in the simulation  optimality_weight (
float
) – controls weighting \(L\) of perfect correlations, seemchammer.calculators.TargetVectorCalculator
 random_seed (
Optional
[int
]) – seed for the random number generator used in the Monte Carlo simulation  tol (
float
) – Numerical tolerance
Return type: Atoms
 cluster_space (

icet.tools.structure_generation.
generate_sqs_by_enumeration
(cluster_space, max_size, target_concentrations, include_smaller_cells=True, optimality_weight=1.0, tol=1e05)[source]¶ Given a
cluster_space
, generate a special quasirandom structure (SQS), i.e., a structure that for a given supercell size provides the best possible approximation to a random alloy [ZunWeiFer90].In the present case, this means that the generated structure will have a cluster vector that as closely as possible matches the cluster vector of an infintely large randomly decorated supercell. Internally the function uses a simulated annealing algorithm and the difference between two cluster vectors is calculated with the measure suggested by A. van de Walle et al. in Calphad 42, 1318 (2013) [WalTiwJon13] (for more information, see
mchammer.calculators.TargetVectorCalculator
).This functions generates SQS cells by exhaustive enumeration, which means that the generated SQS cell is guaranteed to be optimal with regard to the specified measure and cell size.
Parameters:  cluster_space (
ClusterSpace
) – a cluster space defining the lattice to be decorated.  max_size (
int
) – maximum supercell size  target_concentrations (
dict
) –concentration of each species in the target structure (for example
{'Ag': 0.5, 'Pd': 0.5}
Concentrations are always expressed with respect to all atoms in the supercell, which implies that the sum of all concentrations should always be 1. In the case of multiple sublattices, a valid specification would thus be
{'Au': 0.25, 'Pd': 0.25, 'H': 0.1, 'V': 0.4}
.  include_smaller_cells (
bool
) – if True, search among all supercell sizes includingmax_size
, else search only among those exactly matchingmax_size
 optimality_weight (
float
) – controls weighting \(L\) of perfect correlations, seemchammer.calculators.TargetVectorCalculator
 tol (
float
) – Numerical tolerance
Return type: Atoms
 cluster_space (

icet.tools.structure_generation.
generate_target_structure
(cluster_space, max_size, target_concentrations, target_cluster_vector, include_smaller_cells=True, T_start=5.0, T_stop=0.001, n_steps=None, optimality_weight=1.0, random_seed=None, tol=1e05)[source]¶ Given a
cluster_space
and atarget_cluster_vector
, generate a structure that as closely as possible matches that cluster vector. The search is performed among all inequivalent supercells shapes up to a certain size.Internally the function uses a simulated annealing algorithm and the difference between two cluster vectors is calculated with the measure suggested by A. van de Walle et al. in Calphad 42, 1318 (2013) [WalTiwJon13] (for more information, see
mchammer.calculators.TargetVectorCalculator
).Parameters:  cluster_space (
ClusterSpace
) – a cluster space defining the lattice to be decorated.  max_size (
int
) – maximum supercell size  target_concentrations (
dict
) –concentration of each species in the target structure (for example
{'Ag': 0.5, 'Pd': 0.5}
Concentrations are always expressed with respect to all atoms in the supercell, which implies that the sum of all concentrations should always be 1. In the case of multiple sublattices, a valid specification would thus be
{'Au': 0.25, 'Pd': 0.25, 'H': 0.1, 'V': 0.4}
.  target_cluster_vector (
List
[float
]) – cluster vector that the generated structure should match as closely as possible  include_smaller_cells (
bool
) – if True, search among all supercell sizes includingmax_size
, else search only among those exactly matchingmax_size
 T_start (
float
) – artificial temperature at which the simulated annealing starts  T_stop (
float
) – artifical temperature at which the simulated annealing stops  n_steps (
Optional
[float
]) – total number of Monte Carlo steps in the simulation  optimality_weight (
float
) – controls weighting \(L\) of perfect correlations, seemchammer.calculators.TargetVectorCalculator
 random_seed (
Optional
[int
]) – seed for the random number generator used in the Monte Carlo simulation  tol (
float
) – Numerical tolerance
Return type: Atoms
 cluster_space (